rs28940308
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_001127649.3(PEX26):c.265G>A(p.Gly89Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. G89G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127649.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX26 | NM_001127649.3 | c.265G>A | p.Gly89Arg | missense_variant | 2/5 | ENST00000399744.8 | |
PEX26 | NM_017929.6 | c.265G>A | p.Gly89Arg | missense_variant | 3/6 | ||
PEX26 | NM_001199319.2 | c.265G>A | p.Gly89Arg | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX26 | ENST00000399744.8 | c.265G>A | p.Gly89Arg | missense_variant | 2/5 | 1 | NM_001127649.3 | P1 | |
PEX26 | ENST00000329627.11 | c.265G>A | p.Gly89Arg | missense_variant | 3/6 | 1 | P1 | ||
PEX26 | ENST00000428061.2 | c.265G>A | p.Gly89Arg | missense_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 7A (Zellweger) Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2003 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at